trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Overview: Tryptophan biosynthesis in GapMind is based on MetaCyc pathway L-tryptophan biosynthesis (link), from chorismate, glutamine, 5-phosphoribose-1-diphosphate, and serine.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
trpE | anthranilate synthase subunit TrpE | BLP65_RS10660 | BLP65_RS09470 |
trpD_1 | glutamine amidotransferase of anthranilate synthase | BLP65_RS10555 | BLP65_RS00865 |
trpD_2 | anthranilate phosphoribosyltransferase | BLP65_RS10545 | |
PRAI | phosphoribosylanthranilate isomerase | BLP65_RS12585 | BLP65_RS10175 |
IGPS | indole-3-glycerol phosphate synthase | BLP65_RS10540 | |
trpA | indoleglycerol phosphate aldolase | BLP65_RS12575 | |
trpB | tryptophan synthase | BLP65_RS12580 | BLP65_RS05020 |
Alternative steps: | |||
trpED | anthranilate synthase, alpha proteobacterial clade |
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory